Search
Question: TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene name into common gene name
0
gravatar for salvocomplicazioni1
9 months ago by
salvocomplicazioni10 wrote:

I'm trying to analyze TCGA RNA-seq data, so i used TCGAbiolinks, I arrived at normalization data step and i obtained normalized counts matrix, How can I change Ensemble gene name into common gene name?

ADD COMMENTlink modified 8 months ago by tiagochst100 • written 9 months ago by salvocomplicazioni10
1
gravatar for biomiha
9 months ago by
biomiha10
UK/Cambridge
biomiha10 wrote:

I would use biomaRt (https://bioconductor.org/packages/release/bioc/html/biomaRt.html)

ADD COMMENTlink written 9 months ago by biomiha10
1
gravatar for tiagochst
8 months ago by
tiagochst100
Brazil
tiagochst100 wrote:

You have the names inside the SummarizedExperiment object.

 

An example is in this gist:

 

For hg38 the gene names are retrieved with

values(data)$external_gene_name

 

For hg19 

values(data)$gene_id

 

Where data is the summarizedExperiment object, this data was created using biomaRt.

ADD COMMENTlink written 8 months ago by tiagochst100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 126 users visited in the last hour